Acetylcholinesterases--the structural similarities and differences

Acetylcholinesterase (AChE) is a widely spread enzyme playing a very important role in nerve signal transmission. As AChE controls key processes, its inhibition leads to the very fast death of an organism, including humans. However, when this feature is to be used for killing of unwanted organisms (i.e. mosquitoes), one is faced with the question - how much do AChEs differ between species and what are the differences? Here, a theoretical point of view was utilized to identify the structural basis for such differences. The various primary and tertiary alignments show that AChEs are very evolutionary conserved enzymes and this fact could lead to difficulties, for example, in the search for inhibitors specific for a particular species.     

Acetylcholinesterases – the structural similarities and differences

Acetylcholinesterase (AChE) is a widely spread enzyme playing a very important role in nerve signal transmission. As AChE controls key processes, its inhibition leads to the very fast death of an organism, including humans. However, when this feature is to be used for killing of unwanted organisms (i.e. mosquitoes), one is faced with the question - how much do AChEs differ between species and what are the differences? Here, a theoretical point of view was utilized to identify the structural basis for such differences. The various primary and tertiary alignments show that AChEs are very evolutionary conserved enzymes and this fact could lead to difficulties, for example, in the search for inhibitors specific for a particular species.     

New insights on the role of ceramide 1-phosphate in inflammation

Inflammation is a complex biological process involving a variety of locally produced molecules, as well as different types of white blood cells. Some of the so-called inflammatory mediators include cytokines, chemokines, interleukins, prostaglandins, or bioactive lipids, all of which provide protection from infection and foreign substances, such as bacteria, yeast, viruses or some chemicals. Under some circumstances, however, the organism inappropriately activates the immune system triggering an inflammatory response in the absence of foreign insults thereby leading to the establishment of autoimmune diseases. Therefore, inflammation must be tightly regulated in order to ensure sufficient protection to the organism in the absence of unwanted, and at times dangerous, side effects. Increasing experimental evidence implicates sphingolipids as major inducers of inflammatory responses and regulators of immune cell functions. In particular, ceramides and sphingosine 1-phosphate have been extensively implicated in inflammation, and ceramide 1-phosphate has also been shown to participate in these processes. The present review highlights novel aspects on the regulation of inflammation by sphingolipids, with special emphasis to the role played by ceramide 1-phoshate and ceramide kinase, the enzyme responsible for its biosynthesis, in inflammatory responses.     

Ants medicate to fight disease

Parasites are ubiquitous, and the ability to defend against these is of paramount importance. One way to fight diseases is self‐medication, which occurs when an organism consumes biologically active compounds to clear, inhibit, or alleviate disease symptoms. Here, we show for the first time that ants selectively consume harmful substances (reactive oxygen species, ROS) upon exposure to a fungal pathogen, yet avoid these in the absence of infection. This increased intake of ROS, while harmful to healthy ants, leads to higher survival of exposed ants. The fact that ingestion of this substance carries a fitness cost in the absence of pathogens rules out compensatory diet choice as the mechanism, and provides evidence that social insects medicate themselves against fungal infection, using a substance that carries a fitness cost to uninfected individuals.     

Apoptosis: the importance of being eaten

In vivo, cells undergoing apoptosis are usually recognised and swiftly ingested by macrophages or neighbouring cells acting as semi-professional phagocytes. This review debates evidence that the contents of apoptotic cells represent a danger to the organism, being capable of injuring tissue directly or triggering autoimmune responses, concluding that phagocytic clearance of intact apoptotic cells is a safe disposal route. Indeed, new data suggest that, in certain circumstances, phagocytes ingesting apoptotic cells may actively downregulate inflammatory and immune responses. Consequently, increasing evidence that there may be factors capable of perturbing safe clearance of apoptotic cells in vivo suggests that failure of this process may be a hitherto unrecognised pathogenetic factor in inflammatory and autoimmune diseases. New treatments designed to promote safe phagocytic clearance of dying cells can be anticipated, and it may even prove possible to eliminate unwanted cells by inducing appearance of cell surface 'eat me' signals.     

Phage formation in Staphylococcus muscae cultures. IX. Effect of multiple infection on virus synthesis in the absence and presence of specific substrates

1. A strain of S. muscae which requires a substance present in certain acid-hydrolyzed proteins (AHPF) for virus liberation when singly infected in Fildes' synthetic medium no longer needs this substance when multiply infected. 2. In the absence of the AHPF under conditions of multiple infection the amount of phage released is approximately equal to the number of infecting particles between two to ten. Over ten particles per cell has no further effect on the yield of virus. 3. The experimental evidence indicates that it is the phage particle and not some other component in the lysate which can replace the AHPF. 4. The minimum latent period and rise period of cells singly infected in the presence of the AHPF and multiply infected in the absence of the AHPF are the same. 5. The desoxynucleic acid synthesis of cells, infected with a very few virus particles in the presence of excess AHPF and multiply infected with ten particles in the absence of the AHPF, occurs at approximately the same rate, with both infected samples synthesizing about the same amount of desoxynucleic acid and liberating the same yields of virus. 6. A strain of S. muscae which requires aspartic acid for virus synthesis when singly infected does not need this substance when multiply infected, the burst size under the latter conditions depending upon the multiplicity of infection between 3 to 12 particles per cell. 7. The data indicate that the virus released from multiply infected cells in the absence of added AHPF or aspartic acid is newly synthesized virus and not the original infecting particles. 8. The phage particle contains the AHPF and aspartic acid. 9. As a tentative working hypothesis, it is assumed that the AHPF and aspartic acid for phage formation under conditions of multiple infection, in the absence of added AHPF, or of aspartic acid, are contributed by the original infecting particles. 10. Ultraviolet-inactivated phage is adsorbed to the host cell and kills the cell although little virus is released under the experimental conditions. 11. Ultraviolet-inactivated phage particles, if added before the active particle is adsorbed, will greatly inhibit the liberation of new virus particles; but does not do so if added a few minutes after the active particle has been adsorbed. 12. Under the experimental conditions, reactivation of phage when present in multiply infected cells does not occur; and such ultraviolet-inactivated phage cannot serve as a source of the AHPF or aspartic acid, although the AHPF can be liberated from such inactivated particles by acid hydrolysis. 13. The results are discussed in relation to Luria's experiments with ultraviolet-treated phage and to his "gene pool" hypothesis of phage formation.     

San Marco and evolutionary biology

Gould and Lewontin use San Marco, Venice, to criticise the adaptationist program in biology. Following their lead, the architectural term “spandrel” is now widely used in biology to denote a feature that is a necessary byproduct of other aspects of the organism. I review the debate over San Marco and argue that the spandrels are not necessary in the sense originally used by Gould and Lewontin. I conclude that almost all the claims that Gould makes about San Marco are wrong and that it is reasonable to view the architectural spandrel as an adaptation. The spandrels example has not provided a good illustration of why adaptive explanations should be avoided. In fact, it can be used as an example of how adaptive explanations can be dismissed even when there is evidence in their favour. I also discuss the use of the concept of a spandrel in biology.     

Absence of Detectable Mitochondrial Recombination in Paramecium

An extensive search for recombination between mitochondrial markers was carried out in Paramecium tetraurelia. Thirty-two combinations, altogether involving 24 different markers, were studied. The markers belonged to the three main categories of mitochondrial mutations presently available in this organism, (a) Spontaneous or UV-induced antibiotic resistance mutations, most probably affecting mitochondrial ribosomes, (b) nitrosoguanidine-induced antibiotic resistance markers displaying thermosensitivity or slow growth, enabling easy selection of possible wild-type recombinants, and (c) mitochondrial partial suppressors of a nuclear gene, probably corresponding to molecular alterations distinct from the preceding two categories. In addition, different genetic configurations were analyzed (i.e., mutant X mutant, double-mutant X wild-type, etc.).--None of the combinations yielded any evidence for the occurrence of recombined genomes despite the fact that: (1) all of them were studied on a large scale involving the screening of at least several thousand mitochondrial genomes (often several millions), (2) in many of them the detection level was sufficiently high to enable the isolation of spontaneous mutants in control cells, and (3) in several of them, reconstitution experiments carried out in parallel show that the conditions were fully adequate to detect recombinant genotypes. The results are in marked contrast with those obtained on the few other organisms in which mitochondrial recombination has been studied, particularly Saccharomyces cerevisiae, in which mitochondrial recombination is intense.--The most likely basis for the various manifestations of mitochondrial genetic autonomy in Paramecium, described in this as well as in previous publications, is that the chondriome of this organism is made up of thousands of structurally discrete, noninteracting units.     

Deployment of Spatial Attention towards Locations in Memory Representations. An EEG Study

Recalling information from visual short-term memory (VSTM) involves the same neural mechanisms as attending to an actually perceived scene. In particular, retrieval from VSTM has been associated with orienting of visual attention towards a location within a spatially-organized memory representation. However, an open question concerns whether spatial attention is also recruited during VSTM retrieval even when performing the task does not require access to spatial coordinates of items in the memorized scene. The present study combined a visual search task with a modified, delayed central probe protocol, together with EEG analysis, to answer this question. We found a temporal contralateral negativity (TCN) elicited by a centrally presented go-signal which was spatially uninformative and featurally unrelated to the search target and informed participants only about a response key that they had to press to indicate a prepared target-present vs. -absent decision. This lateralization during VSTM retrieval (TCN) provides strong evidence of a shift of attention towards the target location in the memory representation, which occurred despite the fact that the present task required no spatial (or featural) information from the search to be encoded, maintained, and retrieved to produce the correct response and that the go-signal did not itself specify any information relating to the location and defining feature of the target.     

Informatics for protein identification by mass spectrometry

High throughput protein analysis (i.e., proteomics) first became possible when sensitive peptide mass mapping techniques were developed, thereby allowing for the possibility of identifying and cataloging most 2D gel electrophoresis spots. Shortly thereafter a few groups pioneered the idea of identifying proteins by using peptide tandem mass spectra to search protein sequence databases. Hence, it became possible to identify proteins from very complex mixtures. One drawback to these latter techniques is that it is not entirely straightforward to make matches using tandem mass spectra of peptides that are modified or have sequences that differ slightly from what is present in the sequence database that is being searched. This has been part of the motivation behind automated de novo sequencing programs that attempt to derive a peptide sequence regardless of its presence in a sequence database. The sequence candidates thus generated are then subjected to homology-based database search programs (e.g., BLAST or FASTA). These homology search programs, however, were not developed with mass spectrometry in mind, and it became necessary to make minor modifications such that mass spectrometric ambiguities can be taken into account when comparing query and database sequences. Finally, this review will discuss the important issue of validating protein identifications. All of the search programs will produce a top ranked answer; however, only the credulous are willing to accept them carte blanche.     

Absence of evidence is not evidence of absence

Imperfect detection of a species is often a problem when attempting to establish its presence or absence at a set of locations. Failing to find the required evidence that a species is present at a location does not imply that the species is absent, merely that it has not been found. Some of the consequences of imperfect detection is that assessments of factors influencing species presence/absence can be misleading, and how certain can one be that the species is really absent given it has not detected at a location. In this talk I shall briefly review some of the consequences of imperfect detection, methodological advances that enable the detection process to be explicitly accounted for, and practical ways in which the required additional information can be collected.     

The multimeric beta-thymosin found in nematodes and arthropods is not a synapomorphy of the Ecdysozoa

The Ecdysozoa hypothesis proposes a clade of animals including arthropods and nematodes that share the characteristic of periodic molting or ecdysis. The original evidence supporting this hypothesis came from molecular phylogenies based on ribosomal RNA gene sequences. Contrary evidence has come from studies of multiple protein coding genes. One of the most convincing bits of supporting evidence for this theory has been the observation of an unusual multimeric form of the beta-thymosin gene in the genomes of Drosophila melanogaster and Caenorhabditis elegans where, in other metazoans that had been studied, a monomeric form has been found. Here I show that recently deposited sequence data reveal that the multimeric form is in fact a characteristic of all major subdivisions of the Metazoa. The multimeric form is present in a deuterostome, Ciona intestinalis, a lophotrochozoan, Hermissenda crassicornis, and in the ecdysozoans and also exists outside the Metazoa in a fungus. The presence of the multimeric form in nematodes and arthropods, therefore, although not contradicting the Ecdysozoa hypothesis, gives it no support. The absence of the monomeric form in the completely sequenced flies and nematodes may suggest they are linked but, lacking the complete genomes of other ecdysozoans, proving its total absence from the Ecdysozoa is not possible. Furthermore, the absence of the monomeric form from the genome of the deuterostome Ciona suggests that the absence of this character is an unreliable indicator of relationships.     

Efficiency improvement of peptide identification for an organism without complete genome sequence, using expressed sequence tag database and tandem mass spectral data

We compared peptide identification by database (DB) search methods with de novo sequencing results for proteomics study in an organism without genome sequence information. When the former was done by searching the Expressed Sequence Tag (EST) DB of the sample organism or the NCBI nonredundant (nr) protein DB of green plants using either the MASCOT or SEQUEST software program, it was confirmed that the former is as accurate as the latter. Peptides identified from EST DB were twice as many as those from the nr protein DB, in spite of the fact that the EST DB has less data (26 222 EST) than the NCBI nr protein DB (224 238). This study demonstrates that EST DB with tandem mass spectra can be used reliably for high-throughput proteomics studies in an organism without genome information.     

What lies beneath: natural products from marine organisms as nuclear receptor modulators

The consequences for organism fitness of mutations in a given protein are often thought to be determined to a significant extent by epistasis, that is, by the fact that the effect of a mutation may be strongly dependent on the previous mutational background. Actually, a given mutation could be deleterious or beneficial depending on the background, a situation known as 'sign epistasis'. Under pervasive sign epistasis, many mutational trajectories towards a 'fitter protein' will show a 'dip' in fitness and, it has been previously suggested, only a few trajectories will be available to Darwinian selection. In this issue of the Biochemical Journal, Zhang et al. explore how this simple picture needs to be modified when two rather general and important features are taken into account, namely that many proteins are promiscuous and that living organisms must survive and thrive in environments that change continuously. The multidimensional nature of epistasis for a protein involved in several tasks, together with the fact that different tasks may become critical for organism survival as environmental conditions change, is shown by Zhang et al. to contribute to eliminating fitness dead-ends in protein sequence space. Consequently, many alternative mutational trajectories should allow protein optimization for enhanced organism fitness under changing environmental conditions.     

Growth inhibition of Halobacterium cutirubrum by cerulenin,a potent inhibitor of fatty acid synthesis

The polar lipids of $\text{Halobacterium cutirubrum}$ are known to consist exclusively of diether derivatives of glycerol, and do not contain fatty acids. However, cerulenin, a specific and potent inhibitor of fatty acid synthesis, was shown to inhibit the growth of this organism. Protection from growth inhibition was demonstrated when fatty acids of 18 carbons were added to the growth medium, but not when palmitic or palmitoleic acids were used. Cerulenin appears to affect synthesis of all polar lipids in this organism while relative levels of protein and nucleic acids were not significantly affected. Growth inhibition by cerulenin supports the conclusion that the fatty acid synthetase system present in $\text{H. cutirubrum}$ is necessary for lipid biosynthesis, despite the fact that fatty acids are not structural components of the lipids of this bacterium. A pathway is proposed to account for these observations.     

SOP for pathway inference in Integrated Microbial Genomes (IMG)

One of the most important aspects of genomic analysis is the prediction of which pathways, both metabolic and non-metabolic, are present in an organism. In IMG, this is carried out by the assignment of IMG terms, which are organized into IMG pathways. Based on manual and automatic assignment of IMG terms, the presence or absence of IMG pathways is automatically inferred. The three categories of pathway assertion are asserted (likely present), not asserted (likely absent), and unknown. In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding term assigned to it. Automatic pathway inference is an important initial step in genome analysis.     

On the manifestations of memory in visual search

Evidence is presented supporting the thesis that performance in visual search tasks is affected by the contribution of memory processes. Three levels of analysis, corresponding to the various time scales present in a typical search experiment, are discussed. Perceptual learning involves the task and stimulus specific improvement seen across blocks of training. Trial-to-trial priming has an influence which extends over 5-8 trials and lasts on the order of 30 s. Within-trial tagging prevents the re-inspection of already attended (or fixated) items. Also at the within-trial level of analysis, parallel accumulation of evidence for target presence/absence or target location inherently involves memory mechanisms. Organizing the various phenomena in this way makes it apparent that the various mechanisms may interact in a causal way. Within-trial tagging may contribute to priming which may contribute to perceptual learning. Recent proposals that visual search is memoryless (amnesic) are discussed and dismissed.     

On the lack of evidence that non-human animals possess anything remotely resembling a 'theory of mind'

After decades of effort by some of our brightest human and non-human minds, there is still little consensus on whether or not non-human animals understand anything about the unobservable mental states of other animals or even what it would mean for a non-verbal animal to understand the concept of a ‘mental state’. In the present paper, we confront four related and contentious questions head-on: (i) What exactly would it mean for a non-verbal organism to have an ‘understanding’ or a ‘representation’ of another animal''s mental state? (ii) What should (and should not) count as compelling empirical evidence that a non-verbal cognitive agent has a system for understanding or forming representations about mental states in a functionally adaptive manner? (iii) Why have the kind of experimental protocols that are currently in vogue failed to produce compelling evidence that non-human animals possess anything even remotely resembling a theory of mind? (iv) What kind of experiments could, at least in principle, provide compelling evidence for such a system in a non-verbal organism?     

Effects of synthetic defensin fragments on aggregation and adhesion of epitheliolike cells

Normal course of processes of regeneration and epithelization of damaged tissues has been shown to be based on the capability of cells participating in these processes for selective adhesion. In the case of the complete or partial absence of this capability in the cells-participants of the wound healing process, the so-called non-healing wounds appear. In this connection, it remains actual to search for natural agents promoting healing of chronic non-healing wounds. In the present work, we studied effects of synthetic fragments of leukocytic antimicrobial peptides defensines—GER, FGER, and GERA—on aggregation and adhesion of epitheliolike cells of the CHO-K1 line. These peptides have been established to have aggregate-stimulating properties; besides, they enhance adhesion of the cells to the untreated plastic and inhibit fibronectinmediated cell adhesion. Possible pathways of regulation by peptides of processes of intercellular and cell-matrix interaction are discussed as well as ways of release of these compounds in an organism and their functional role in an organism.     

Effects of synthetic fragments of defensins on aggregation and adhesion of epitheliolike cells

Normal course of processes of regeneration and epitheliazation of damage tissues has been shown to be based on the capability of cells participating in these processes for selective adhesion. In the case of the complete or partial absence of this capability in the cells-participants of the wound healing process, the so-called non-healing wounds appear. In this connection, it remains actual to search for natural agents promoting healing of chronic non-healing wounds. In the present work, we studied effects of synthetic fragments of leukocytic antimicrobial peptides defensines--GER, FGER, and GERA--on aggregation and adhesion of epitheliolike cells of the CHO-K1 line. These peptides have been established to have aggregate-stimulating properties; besides, they enhance adhesion of the cells to the untreated plastic and inhibit fibronectinmediated cell adhesion. Possible pathways of regulation by peptides of processes of intercellular and cell-matrix interaction are discussed as well as ways of release of these compounds in an organism and their functional role in an organism.